I haven't read every post on this thread thoroughly, so please forgive if I'm missing something, but it looks like your just seeing the effect of caching. Logging out does not drop your buffers from the cache.

Pay attention to the second query. It ran for 15 or so seconds, did lots of db file sequential read, and then subsequent executions did not. I disconnected, reconnected again, and the query ran quickly. I disconnected again, reconnected, and got a good plan once again. I can provide that 10046 as well.

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